Assalam o alaikum everyone ,, I want to extract genes information from annotation files (gff). I have gff files of different genomes downloaded from NCBI and two txt files 1 of them contains full path of gff files and 2nd contains list of genes which information have to extract from annotation files. $ cat annotation_files_path ~/home/usr/NCBI_Mammals_genomes/Nine_banded_armadillo/ ~/home/usr/NCBI_Mammals_genomes/Noth_American_deer_mouse/ 

#!usr/bin/perl
#
# read genes into array
#
my @ARGV = [];
my $genesFn = "Genes_list.txt";
open my $genesFh, "<", $genesFn or die "could not open genes file hand
+le!\n";
while (<$genesFh>) {
    chomp;
    push @ARGV, $_;
}


#
# write any matches between annotation line and pattern to results fil
+e
#
my $annotationsFn = "GCF_000298275.1_OryAfe1.0_genomic.gff";
my $resultsFn = "answer.gff";
open my $annotationsFh, "<", $annotationsFn or die "could not open ann
+otations file handle!\n";
open my $resultsFh, ">", $resultsFn or die "could not open handle to r
+esults file!\n";
while (<$annotationsFh>) {
    chomp;
    if ($_ =~ /ACMSD/ || $_ =~ /CRYM/ || $_ =~ /ARID1B/  {
        print $resultsFh " $_\n";
    }

close $resultsFh;
close $annotationsFh;
close $genesFh;

[download]

I have two problems now first one is that all genes information come in a single file but i want different output file for different genes and if gene not present it should be mentioned,, and second and major problem is that i have to work on about 100 annotation files and in annotation_file_path.txt i gave complete path of all annotation files but failed to execute it because script only work when a single annotation file use as shown above otherwise it print whole annotation _file_path.txt ,,, is there any way to open each path of annotation_file.txt one by one ??? kindly guide me ??? i'm a beginner so happy to give me more info..

In reply to perl script for extracting gene information from gff file by Anonymous Monk

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